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I'd say that the only difference is that the form ending in -se can be considered slightly more formal than the one ending in -ra; but otherwise (i.e., regarding the meaning) they are equivalent.
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Gonzalo MedinaNov 22 '11 at 22:53

There is no difference in meaning. I have found that the -ra endings are more common in Latin American Spanish and the -se endings are more common in European Spanish. So I would use the one that represents the type of Spanish you are trying to speak.

What about Mexico, which is in North America? If it falls in with Central and South America (which it often doesn't) you can just use the term "Latin American Spanish" instead.
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hippietrailNov 23 '11 at 0:18

When used as subjunctive, there is no difference in meaning, except that as noted, the -se forms can carry in some places a slightly elevated sound, and regional/personal/phonetic differences will also affect the choice. (-se frankly just sounds better on some verbs, on -ra on others).

But, do note that the -ra forms can also be used in the indicative, where they form the simple pluperfect: Ya se levantara cuando recibió la llamada. Thus it is possible —although very rebuscado given how little -ra is used in the indicative— to have a sentence where -se is the only unambiguously subjunctive form: El estudiante hacía lo que la profesora indicara (does indicara mean había indicado or indicase? Could be either.)